Building Skills in Python: A Programmer’s Introduction to Python by Steven F. Lott (© 2002, 2005, 2007, 2008 Steven F. Lott).

screen is a must-use for anyone familiar with SSH sessions; it saves your time by keeping your console apps running even after (an unexpected) disconnect from the remote session.

The easiest way to start with screen is screenie – an interface to screen. To use it, you only need to memorize a single keyboard shortcut: C-a d (Ctrl+a, d). This shortcut detaches (hides) your current screen session, allowing to resume later – either with the help of screenie, or by issuing screen -r command.

After a while, with increased screen (and screenie) usage, you will find it inconvenient detaching every time you need a new screen session. Here comes the second keyboard shortcut: C-a c (Ctrl+a, c), which creates a new window within a current screen session, and switches to it.

Finally, you will find it tiresome detaching to then re-attach to a different screen. C-a “ (Ctrl+a, Shift+’) will display a list of screen windows for you to select and switch to.

Screenie, an excellent beginner’s interface to screen, is no longer needed after you memorize these 3 keyboard shortcuts.

Many will say that this is a bare minimum, and also there is much more to screen than what you present here, and that will be true. However, these 3 shortcuts are sufficient for simple but convenient everyday screen sessions management.

There is an excellent step-by-step instruction on resetting the bad clusters counter of an NTFS partition with linux-ntfs tools. I’ve checked – it works as expected:

1. Back up important data from partition just in case
2. Find out size of ‘$Bad’ attribute in $Badclus using ntfsinfo -i 8 partition (partition is for example /dev/sda1). It will be the “Allocated size” value in the “Dumping attribute $DATA (0×80)” (there will be two 0×80 attributes. Only one has an “Allocated size” line). Let us write down (remember) this size as ntfs_size.
3. Use ntfstruncate partition 8 0×80 ‘$Bad’ 0 to set $Bad’s attribute length to zero.
4. Use ntfstruncate partition 8 0×80 ‘$Bad’ ntfs_size to set $Bad’s attribute length back to proper value ntfs_size which was recorded in step 2.
5. Boot into Windows and run chkdsk -f diskname. It will find errors and should fix them.

However, Debian’s ntfsprogs package does not have the ntfstruncate binary.

Here’s how you can easily build one yourself (you may need a few extra packages with build tools for that):

1. apt-get source ntfsprogs
2. cd linux-ntfs-2.0.0
3. ./configure && make extra
4. cd ntfsprogs && ./ntfstruncate

You can also install ntfstruncate system-wide, but I have no idea if that will interfere with the already-installed ntfsprogs package, so I just used this binary directly from linux-ntfs-2.0.0/ntfsprogs.

Bad clusters happen not only when cloning an NTFS partition between 2 physical hard disk drives. Once, after a brief blackout (with a turned on PC, and not on a UPS), the SMART status of my new HDD started showing 1 ‘Pending sector’. Correspondingly, all the SMART tests (performed with a smartctl utility) reported read errors. To help my HDD examine and fix the problem itself, I performed a write operation to that single unreadable sector, which restored it (and reset the ‘Pending sector’ counter back to zero). It was possible, because not the physical sector itself, but the hidden CRC field had errors after power failure; modern hard drives can detect and fix this kind of errors upon write operations (read operations only mark the sector as ‘pending’, because data read is not consistent with the stored CRC).

However, NTFS partition still had 4096 bytes in ‘bad clusters’. A little research revealed the presence of internal NTFS bad clusters counter, which can be reset following the procedures above.

“We only value what we loose”, they say.

Fortunately, I haven’t lost anything valuable, and don’t plan to. However, I did come to realize that false leads may and actually do obscure some simple happiness bits we fail to notice in our everyday life. Especially when that happiness comes from someone close, someone you literally got used to as to something inseparable from your life – but still fail to give value to.

Take care of your happiness and inner peace – do stop sometimes to thank and praise and value the oh-so-inseparable people around you.

Copyrights note: this is not my image, and I do not know who is the proper copyrights holder. It is used here for illustrative non-profit purposes, with a proper disclaimer. Contact me if you own the copyright and wish this image removed.

Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom margin of microarray sensitivity, and anything below that margin cannot be reliably quantified - which also means that both fold-change and p-value of expression variance will be unreliable for these probesets.

Here's a simple R script to do just that. It is abundantly commented, and also contains an optional (commented out) fragment which allows the removal of more low-variance, low-intensity probesets.

Hint: click the "plain text" box header to be able to right-click the code, "Select All", and then "Copy".

Sample use:

> source("script.R")
> expr.filtered = filter_below_spikes(eset)

Comments and suggestions are welcome.

Recently, I have come across the Chandler project. Chandler is a sophisticated organizer, including tasks, calendar, appointments, invitations, and many more.

The project does provide a 64-bit package for Ubuntu 8.10 "Intrepid Ibex", but it has a dependency on python-zope-interface - which in Debian testing is a virtual package, currently provided by python-zope.interface. That single dependency made my aptitude complain all the time, so I edited the .deb-file, renaming depends/python-zope-interface to depends/python-zope.interface (following nice and simple instructions). After that - no more aptitude complaints, and Chandler works fine.

Download the modified Chandler 1.0.3 Debian testing amd64 package (md5: 239071715977bea2eb75f3bb54491a02).

MathIsFun offers nicely illustrated pages on math, algebra, geometry and maybe more.

For example, there is a step-by-step instruction on calculating variance and standard deviation for a set of measured dog heights, with a final picture (below) illustrating one-sigma distance from the mean. Unfortunately, concepts of normal distribution and %% of data points within each sigma range are not discussed, but that might as well be too much for a nice explanation. There are also animations, like this mean machine. Overall, MathIsFun is a nice resource for younglings.

Just a quick note: upgrading Drupal using a patch file is a really efficient and fast method, especially because diff/patch files are available for different Drupal version combinations.

For about 2 weeks now, I am every day alerted of the suspicious behavior of some computer/server from the Google's IP range:

Dec 5 05:39:33 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[option]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:33 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[Itemid]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:33 mx suhosin[3701]: ALERT - tried to register forbidden variable 'GLOBALS' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:33 mx suhosin[3701]: ALERT - ASCII-NUL chars not allowed within request variables - dropped variable 'mosConfig_absolute_path' (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[option]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - tried to register forbidden variable '_REQUEST[Itemid]' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - tried to register forbidden variable 'GLOBALS' through GET variables (attacker '66.249.71.20', file 'html/index.php')
Dec 5 05:39:42 mx suhosin[3701]: ALERT - ASCII-NUL chars not allowed within request variables - dropped variable 'mosConfig_absolute_path' (attacker '66.249.71.20', file 'html/index.php')

These requests repeat up to several hundred times per hour, with periods of no or very little malicious requests.

Here's WHOIS information about 66.249.71.20:

OrgName: Google Inc.
OrgID: GOGL
...
NetRange: 66.249.64.0 - 66.249.95.255
CIDR: 66.249.64.0/19
NetName: GOOGLE
NetHandle: NET-66-249-64-0-1
Parent: NET-66-0-0-0-0

Does Google attack you, too?

These attacks initially started from a different Google IP - 66.249.71.2; I wrote to abuse at google, and got an automated response with the ticket number (in the hundreds of millions range). A week after that, requests started flowing from IP 66.249.71.20. I am not inferring "evil Google abuse department" here, just that there was no response, and the problem shifted to a different IP from the Google's IP range.

Update: I decided just to ignore this.

"Evil?" image by copyblogger.com.

fail2ban has a php-url-fopen rule.

WordPress has a Global Translator plugin, which - among others - uses Google Translate service.

If someone uses Google Translate (e.g. using Global Translate's mini-language-flags), and goes back to your blog - that someone might get banned by fail2ban (especially if you have set maxretry to 1), as the referrer will contain the php-URL-fopen attack signature. The bad thing is that you will not realize that until after you check one or several translations yourself, as a random site visitor experiencing the problem is highly unlikely to bother reporting this problem - especially when your blog's Contact page is also inaccessible.

Clearly, Google Translate is not the only legitimate service which will trigger that rule.

Solution: The only solution I have found is to specify the whitelist regex for the php-URL-fopen rule.

A nice report on the cost of bruteforcing variable-length and variable-complexity passwords using cloud computing services (e.g. Amazon's EC). There's a kind of a tutorial in their previous post.

Slow DoS attack with just 1 computer against a number of web servers, including Apache: slowloris. There is a solution for Apache, packaged for RedHat and also available for Debian.

Finally, there's Go programming language. The most inspiring promise to me personally is the ease of execution parallelization with language's built-in syntactic constructs. That is something highly desired. Also, I like that it is a compiled language. However, it might be 10%-20% slower than pure C. Let's see how it grows.

ocrodjvu = OCRopus (tesseract) + DJVU

It is a small command-line tool to easily convert your image-only DJVU files into image+text DJVU files. In Debian testing, there are language packages for (in no specific order) German, English, French, Spanish, Vietnamese, Brasilian Portuguese, Dutch, and Italian. The original tesseract-ocr software includes training data & code, so it should be (at least in theory) easy to add more recognition languages.

Starting October, 30, there is a 3-week quarantine in all primary and higher bodies of education in Ukraine - to limit the spread of the infection.

A total of 80k people were registered with respiratory infections (not classified by flu type). Several small samples tested for A/H1N1 (which is the cause of swine flu pandemic) indicate that 30-50% of all cases could be swine flu (with other cases being "seasonal flu" - that is, previously known influenza types and subtypes). It is reported that ~37 died since Monday, with symptoms matching those of swine flu. Most of the statistics come from the Western regions of Ukraine, which were the first to face rapid daily temperatures decrease - which could have been the trigger of massive infections.

Today I've seen a number of people in Kyiv's underground railway wearing medical face masks (or just pulling their scarfs up to cover noses). Drug stores were literally stormed for anti-virus medications, immune system stimulators, medical face masks, vitamins, etc.

If not the virus, then panic is definitely in the air. I do not recollect seeing something like that before.

This query performs a table-wide search-and-repalce:

UPDATE `table_name` SET `table_field` = REPLACE(`table_field`,'string to search for and replace','replacement string');

If you need a database-wide search-and-replace, you could try this script (I haven't tested/used it myself).

Beware of the following gotchas:

1. wrong query syntax may ruin the field you are performing replace on, so always backup first!
2. be sure to provide "search-for" string as specific as possible, or you will get unexpected replacements (e.g. replacing mini with little will also convert all minivans into littlevans); also, do use WHERE clause when necessary to limit the number of rows modified
3. the function in the example is case-sensitive, so replacing all minivans with vehicles won't replace Minivans. However, I believe there exists a case-insensitive version of REPLACE function

Production: see http://www.howtoforge.com/how-to-set-up-apache2-with-mod_fcgid-and-php5-on-debian-etch - it is for Debian Etch (which is old-stable), but many of the steps apply equally well to Debian Lenny (current-stable). Also, this is a very basic guide, as if you are going to host multiple sites from multiple clients, you most definitely will need some hosting control panel.

Development: see http://www.ruzee.com/blog/2009/01/apache-virtual-hosts-a-clean-setup-for-php-developers. This setup works very well, unless you need to create several virtual hosts every day - in which case necessary actions could be partially scripted.

If you get this message when opening vignettes:

Error in openPDF(vif) :
getOption('pdfviewer') is ''; please use 'options(pdfviewer=...)'

and you are tired of running this command every time:

> options(pdfviewer="okular")

then you should check if your system-wide Renviron file has proper PDF viewer set:

grep -i pdf /etc/R/Renviron

R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-'/usr/bin/pdflatex'}}
R_RD4PDF=${R_RD4PDF-'times,hyper'}
## Default PDF viewer
R_PDFVIEWER=${R_PDFVIEWER-''}

It wasn't in my case.

To set one, either edit the system-wide Renviron (e.g. by editing the R_PDFVIEWER=${R_PDFVIEWER-''} line to look like R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/xdg-open'} - this will use MIME types to open your preferred PDF viewer), or one of the per-user/per-directory Renviron files to fix this minor annoyance (format is the same, e.g. R_PDFVIEWER=okular ).

PwdHash uses your "single password" to create a site-unique password (by making a one-way hash of your password and the site's domain).

Although I'm not using "single password for all sites", PwdHash does look very convenient.

Regular expressions (regexps) are powerful indeed. But debugging non-trivial regexps is a burden even if you understand how regexps work, and remember most (if not all) regexp syntax.

Miscellaneous tools exist to ease this task. This post was inspired by redet's comparison of regexp helper tools - it could be sufficient to read only that, if you're going to try the mentioned tools yourself. Otherwise, read on.

Kodos is an easy-to-use (but powerful enough) Python tool to verify regular expressions against sample user-provided strings. Available for both Linux and Windows. Generates ready-to-use Python regexp code.

redet assumes some knowledge of REs. Unlike all the other helper tools, it has the widest code generation coverage - just go to "Tools->Save command information" to generate code (Python, Perl, C, grep - just to name a few of the 57 (!) languages/tools/editors supported). At the same time, redet does not depend on specific versions of all supported RE engines - instead, redet automatically tests for features in available versions.

visual-regexp is similar to kodos in features.

txt2regex is a regex wizard written in bash, capable of generating code for 24 languages/editors/programs (by default, these are enabled: perl, php, postgres, python, sed and vim). It is really simple and convenient, though some understanding of "groups" and "character ranges" is highly recommended.

KRegExpEditor was a part of kde3-utils, and seems to be missing from current KDE 4.3. It is similar to kodos and visual-regexp in its philosophy and features.

I would recommend using one of kodos/visual-regexp/kregexpeditor to quickly test or design your regular expression, then use redet to generate appropriate source code. As an alternative (and when working in a console), just use txt2regexp to generate the code you need.

Tools I haven't tried include regex coach and regexpviewer.

Please also see this extensive list of regular expression and pattern-matching related software.

Today Google celebrates the invention of the barcode.

To help in this celebration, you can make a barcode with your site's address (there is at least one more at barcodesinc, but at the moment of writing it is painfully slow).

I find these parameters nearly optimal:

• Type: Code 128-B
• Styles: Draw value text
• Size: 234x60 (half-banner size)
• Xres: 1
• Text font: 5
• Value: bogdan.org.ua

If you wish, you can also exactly replicate today's Google logo - which says "Google", as you could have guessed.

You can place this barcode on your "souvenirs" - pens, cups, t-shirts. Many phones now have barcode scanners (e.g. Nokia E71), so put this code onto your namecard.

Read on to learn about matrix barcodes.

You may also investigate further into matrix/2D codes, which may contain much more information. To the left is the QR code of my blog's address - try and scan it with your cameraphone! Or make one for yourself.

Here's an encrypted message:

There are many types of matrix/2D barcodes. QR code (above), datamatrix (left picture) and Semacode (right picture) were all successfully recognized by my phone.

If you have happened to observe similar messages in your dmesg:

[ 0.004000] Checking aperture...
[ 0.004000] No AGP bridge found
[ 0.004000] Node 0: aperture @ 20000000 size 32 MB
[ 0.004000] Aperture pointing to e820 RAM. Ignoring.
[ 0.004000] Your BIOS doesn't leave a aperture memory hole
[ 0.004000] Please enable the IOMMU option in the BIOS setup
[ 0.004000] This costs you 64 MB of RAM
[ 0.004000] Mapping aperture over 65536 KB of RAM @ 20000000

and you are using AMD-based system w/o AGP video, then my advice is: just leave that as is, do not bother "improving"! Any tinkering with kernel boot options won't do you any good, as the kernel has already done the best it could.

Just a note: all those messages at the top of the post should only happen if you have 4 or more GiBs of RAM. If you have less than that, and do have those messages – my experience might be inappropriate for your case.

Another note: my BIOS does not have any IOMMU settings (or “Memory hole remapping” settings), so I didn’t try that. You should check if your BIOS has IOMMU-related options first, just as kernel message suggests.

Read on for details.

My system's kernel at the moment of writing is 2.6.30-1-amd64 (Debian testing), running on MSI's 790GX-G65 with integrated Radeon HD 3300 video, with 4 GiB DDR3 RAM and a quad-core Phenom II CPU.

Following are the options you shouldn't try on a similar system:

• passing iommu=noagp kernel boot option. If you run dmesg|grep -i agp, most likely you will see something in the lines of
  

  $ dmesg|grep -i agp
  [ 0.004000] No AGP bridge found
  [ 0.392098] PCI-DMA: Disabling AGP.
  [ 0.392142] PCI-DMA: Reserving 64MB of IOMMU area in the AGP aperture
  [ 0.774847] Linux agpgart interface v0.103

  which tells you that your kernel has automatically discovered the absence of AGP bridge, disabled it and is using 64MB of AGP aperture for IOMMU. On my system, adding that boot option had no effect.

• passing iommu=off kernel boot option. When I did this, there were loads of "nommu overflow" errors during boot, so I didn't wait until GDM start and rebooted immediately. Clearly, tons of "overflow" errors won't do any better than a harmless "This costs you 64 MB of RAM". Also, systems with over 3 GiB RAM do need IOMMU.
• passing iommu=noaperture kernel boot option. On my system, this option has taken 1 more MiB from my available RAM (as reported by free -m or htop), and also enabled software double-buffering IOMMU method (in dmesg, a string similar to SW TIOLB). Performance-wise this is worse than AMD's GART-based IOMMU, and you loose 1 more MiB of RAM , so don't do this.
• passing iommu=noagp,noaperture for me had the same effect as passing iommu=noaperture alone, for the reason from point #1 of this list.
• I haven't tried any of the memaper=[1|2|3|...] options, as I had no problems with the default 64 MiB.
• passing mem=4G may remove that message (I do not recollect if it did for me), but will eat a good deal more of your available RAM (might be because devices are now mapped within those 4G, and not above). So don't do this.

I'm not aware of any other solutions to the missing 64 MiB RAM message. There were notices of using pci=nommconf boot option, but that is too much for such a simple message - unless you have problems booting.

Below I'm pasting IOMMU-relevant part of the linux-source-2.6.30/Documentation/x86/x86_64/boot-options.txt file, which I believe is the source of ultimate knowledge You should read that file whenever you feel like tinkering with boot options of your AMD64 machine.

I ***highlighted*** some fragments, to support the points from the list above.

IOMMU (input/output memory management unit)

 Currently four x86-64 PCI-DMA mapping implementations exist:

   1. : use ***no hardware/software IOMMU at all***
      (e.g. ***because you have < 3 GB memory***).
      Kernel boot message: "PCI-DMA: Disabling IOMMU"

   2. : ***AMD GART based hardware IOMMU***.
      Kernel boot message: "PCI-DMA: using GART IOMMU"

   3.  : Software IOMMU implementation. Used
      e.g. ***if there is no hardware IOMMU*** in the system and it is need because
      you have ***>3GB memory*** or told the kernel to us it (iommu=soft))
      Kernel boot message: "PCI-DMA: Using software bounce buffering
      for IO (SWIOTLB)"

   4.  : IBM Calgary hardware IOMMU. Used in IBM
      ***pSeries and xSeries servers***. This hardware IOMMU supports DMA address
      mapping with memory protection, etc.
      Kernel boot message: "PCI-DMA: Using Calgary IOMMU"

 iommu=[][,noagp][,off][,force][,noforce][,leak[=]
	[,memaper[=]][,merge][,forcesac][,fullflush][,nomerge]
	[,noaperture][,calgary]

  General iommu options:
    off                Don't initialize and use any kind of IOMMU.
    noforce            Don't force hardware IOMMU usage when it is not needed.
                       (default).
    force              Force the use of the hardware IOMMU even when it is
                       not actually needed (e.g. because < 3 GB memory).
    soft               Use software bounce buffering (SWIOTLB) (default for
                       Intel machines). This can be used to prevent the usage
                       of an available hardware IOMMU.

  iommu options only relevant to the AMD GART hardware IOMMU:
                 Set the size of the remapping area in bytes.
    allowed            Overwrite iommu off workarounds for specific chipsets.
    fullflush          Flush IOMMU on each allocation (default).
    nofullflush        Don't use IOMMU fullflush.
    leak               Turn on simple iommu leak tracing (only when
                       CONFIG_IOMMU_LEAK is on). Default number of leak pages
                       is 20.
    memaper[=]  Allocate an own aperture over RAM with size 32MB<4GB.
                       DAC is used with 32-bit PCI to push a 64-bit address in
                       two cycles. When off all DMA over >4GB is forced through
                       an IOMMU or software bounce buffering.
    nodac              Forbid DAC mode, i.e. DMA >4GB.
    panic              Always panic when IOMMU overflows.
    calgary            Use the Calgary IOMMU if it is available

  iommu options only relevant to the software bounce buffering (SWIOTLB) IOMMU
  implementation:
    swiotlb=
[,force]
            Prereserve that many 128K pages for the software IO
                       bounce buffering.
    force              Force all IO through the software TLB.

  Settings for the IBM Calgary hardware IOMMU currently found in IBM
  pSeries and xSeries machines:

    calgary=[64k,128k,256k,512k,1M,2M,4M,8M]
    calgary=[translate_empty_slots]
    calgary=[disable=]
    panic              Always panic when IOMMU overflows

    64k,...,8M - Set the size of each PCI slot's translation table
    when using the Calgary IOMMU. This is the size of the translation
    table itself in main memory. The smallest table, 64k, covers an IO
    space of 32MB; the largest, 8MB table, can cover an IO space of
    4GB. Normally the kernel will make the right choice by itself.

    translate_empty_slots - Enable translation even on slots that have
    no devices attached to them, in case a device will be hotplugged
    in the future.

    disable= - Disable translation on a given PHB. For
    example, the built-in graphics adapter resides on the first bridge
    (PCI bus number 0); if translation (isolation) is enabled on this
    bridge, X servers that access the hardware directly from user
    space might stop working. Use this option if you have devices that
    are accessed from userspace directly on some PCI host bridge.

Screem HTML/XML editor has tag-specific auto-complete, and is a nice editor for web-developers (at least as long as Quanta is not available for Debian testing).

However, version 0.16.1 is very unstable, and dies with

***MEMORY-ERROR***: screem[5527]: GSlice: assertion failed: sinfo->n_allocated > 0

As a workaround (initially suggested for the highly similar Firestarter crashes), try running screem with this command:

G_SLICE=always-malloc screem

Too bad last development version of Screem is dated March 2006.

DIYbio is

an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.

DIYbio also has a google group, where a wide range of questions - from bio-patents to DIY gel electrophoresis shopping list and model organisms is dicussed. There is also a DIYbio/biohacking FAQ.

Today for me is the day of discoveries. I learned about the International Open Space Initiative (to give robotics enthusiasts a way to send their tele-controlled and/or intelligent robots to the Moon and Mars), about the DIYbio and biohackers, about OpenManufacturing (which doesn't seem to have produced enough content to link to), Open Source Medicine (ouch!), BioBrick Assembly Kit (with an assembly manual), OpenWetWare, and a whole bunch of other awesome and inspiring community efforts, which do not belong here.

Do you feel the wind of change?

This will be the 2nd DrupalCamp in Kyiv. Please click the logo to visit the official web-site to learn more.

Stumbled upon SciVee.TV - an open video upload service for research-related videos.

I believe it is highly useful. Compare: watching an 8-10 minute video of someone's research to reading their article on that same subject. For me, those 8-10 minutes make video option a clear winner.

One of the envisioned uses of SciVee is to upload videos describing peer-reviewed published articles. This has two benefits for the reader: quickly getting acquainted with the essence of the article, and having that article as a complete reference for any questions not discussed in the video. For the author, this gives an additional bonus of higher visibility of his research.

Personally, I've immediately found 3 videos pertinent to my topic. Of those, one was accompayning an article in PloS Biology, one was an hour-long lecture, and one was a poor quality audio recording of someone's intended research.

SciVee is young, and that is currently the largest drawback: not much could be found in a narrow research field. But I'm sure it will grow.

The two graphs below (clickable) are for CPU and RAM use during a period of a program going wild between 23:17 and 23:41 (24+ minutes of server's downtime). The program was run non-root, it just consumed all the memory it could. It was killed by kernel, so the server started responding without any interventions - which were hard to perform, because none of the services (including ssh) were responding during downtime.

If you happen to be developing a C/C++ program - do use mtrace and valgrind, those are huge helpers against the problems akin to that shown on the graphs.

I have read manpages of rsync today.
I feel enlightened.

I had a dream of rsync being one of the legendary nix Super-Cows.

A tiny perversive part of self created a PDF version of rsync manpages.

It seems that Super-Cows can damage the brain, when stared at too intensely.

If you ever need to glimpse at the properties of the Poisson distribution with lambda=0.16, or find the factorial of 6163338 (as a gamma function), then Wolfram|Alpha is a perfect tool for you (unless you have some math package at hand).

The motto of Wolfram|Alpha is Making the world's knowledge computable. Basically, it is like Mathematica plus a growing corpus of factual numeric data, plus a system to interpret user's input. This is a nice online reference and computation platform.

Recently, I have come across an excellent piece of advice called Ten simple rules for getting published. The only thing I have to add is that final rule #10 should be kept in mind while checking through all the previous rules - e.g. when editing someone's submission, make sure that you are in position to be the editor for that article, and make sure your decision will influence chief editor's decision - otherwise there's no use reviewing.

PLoS Computational Biology, where the "simple rules" were published, has a Ten simple rules collection, which includes a handful of other useful advice articles, like 10 simple rules for selecting a postdoctoral position.

Here's the ultimate proof :

One can clearly see that on weekends the number of unique visitors of my blog drops drastically to about 40-50% of the working week average.

And yes, that is an almost perfect 5+2 pattern, which I'm observing for many months, like a week-long circadian rhythm. "Almost perfect" must be due to the differences in time zones.

I wonder if the same pattern is characteristic for most web-sites... That is, if people mostly do the browsing at work, and not at home.

Anybody wants to share the secret cycles of one's blog audience?

There is no way I'm aware of to do what the title says. However...

I'm sure that you are aware of the fact that floats representation in any programming language is limited by the precision of the internal binary representations. In other words, you can never have an exact float representation - there will always be some precision associated with the float you are working with. The simplest example is the difference in precision between the float and double types in C.

Suppose I have the following code fragment:

Both result.score and input->raw_cut_off are of type float, and can have positive and negative values. When compared with the greater than or equal ( >= ) operator, it is not always that condition is true - for the precision reasons shortly mentioned above.

As I already said, there is no precision specification for equality operators in C. But it is quite simple to "invent" precision specification; e.g. if I wanted to test for equality only, I could write

In this example, I'm effectively asking for 6-digit precision for the equality comparison of floating-point values. Note, that if you replace that 0.000001 with the actual precision limit of the floating type you are using, you will be "exactly" comparing floating-point numbers - up to that type's precision, of course .

The first-most example with the >= operator can be rewritten as

where precision is exactly what it is named, e.g. precision = 0.000001.

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• comment by Randy A. Ynchausti
• scientific programming